This is an automatically-produced report from shinyQC. The analyzed data contains 630 features and 88 samples.

1 Tab: Samples

1.1 Histogram

Use the settings

  • Categorical variable = name.

1.2 Mosaic

The mosaic plot was not called within the shiny application. Use default settings.

Use the settings

  • Categorical variable 1 = name and
  • Categorical variable 2 = name.

2 Tab: Measured Values

2.1 Barplot for samples

2.2 Histogram Features

The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Binwidth = 1.

2.3 Histogram Features along variable

The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Variable for stratification = name and
  • Binwidth = 1.

2.4 UpSet

The ‘Upset’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Variable for stratification = name.

3 Tab: Missing Values

3.1 Barplot for samples

3.2 Histogram Features

The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Binwidth = 1.

3.3 Histogram Features along variable

The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Variable for stratification = name and
  • Binwidth = 1.

3.4 UpSet

The ‘Upset’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Variable for stratification = name.

4 Tab: Intensities

4.1 Boxplot/Violin plot

Use the settings

  • Display log2 values? = FALSE and
  • Type of display = FALSE.

4.2 Trend/drift

Use the settings

  • Select variable = ,
  • Select level to highlight = ,
  • Select data input = raw,
  • Select aggregation = sum,
  • Select smoothing method = loess, and
  • Select variable to order samples = .

4.3 Coefficient of variation

4.4 Mean-sd plot

4.5 MA plot

The ‘MA plot’ was not called within the shiny application. Use default settings.

Use the settings

  • group = all,
  • plot = all,
  • Data set for the MA plot = raw, and
  • lines = FALSE.

4.6 ECDF

The ‘ECDF’ plot was not called within the shiny application. Use default settings.

Use the settings

  • Data set for the ECDF plot = raw,
  • Sample = 1_Plasma_4C_0_C1, and
  • group = all.

4.7 Distance matrix

The ‘Distance matrix’ plots were not called within the shiny application. Use default settings.

Use the settings

  • annotation = name and
  • distance method = euclidean.

5 Tab: Dimension Reduction

5.1 PCA

The ‘PCA’ plot was not called within the shiny application. Use default settings.

Use the settings

  • x-axis = PC1,
  • y-axis = PC2,
  • scale = TRUE,
  • center = TRUE, and
  • Highlight = none.

5.2 PCoA

The ‘PCoA’ plot was not called within the shiny application. Use default settings.

Use the settings

  • x-axis = Axis.1,
  • y-axis = Axis.2,
  • Distance measure = euclidean, and
  • Highlight = none.

5.3 NMDS

The ‘NMDS’ plot was not called within the shiny application. Use default settings.

Use the settings

  • x-axis = MDS1,
  • y-axis = MDS2,
  • Distance measure = euclidean, and
  • Highlight = none.
## Run 0 stress 9.8761e-05 
## Run 1 stress 9.754276e-05 
## ... New best solution
## ... Procrustes: rmse 2.886935e-05  max resid 0.0001422001 
## ... Similar to previous best
## Run 2 stress 9.86572e-05 
## ... Procrustes: rmse 1.153469e-05  max resid 3.100026e-05 
## ... Similar to previous best
## Run 3 stress 9.594461e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001095138  max resid 0.0003442642 
## ... Similar to previous best
## Run 4 stress 9.597091e-05 
## ... Procrustes: rmse 5.576928e-05  max resid 0.0003360568 
## ... Similar to previous best
## Run 5 stress 9.972704e-05 
## ... Procrustes: rmse 0.0001139659  max resid 0.0003331439 
## ... Similar to previous best
## Run 6 stress 0.0001031675 
## ... Procrustes: rmse 0.0001307271  max resid 0.0003813627 
## ... Similar to previous best
## Run 7 stress 9.736016e-05 
## ... Procrustes: rmse 0.0001224382  max resid 0.0003583916 
## ... Similar to previous best
## Run 8 stress 9.986547e-05 
## ... Procrustes: rmse 0.0001047054  max resid 0.0003592288 
## ... Similar to previous best
## Run 9 stress 9.13122e-05 
## ... New best solution
## ... Procrustes: rmse 6.509991e-05  max resid 0.0002655749 
## ... Similar to previous best
## Run 10 stress 9.823867e-05 
## ... Procrustes: rmse 0.0001081686  max resid 0.000279633 
## ... Similar to previous best
## Run 11 stress 9.778621e-05 
## ... Procrustes: rmse 6.981572e-05  max resid 0.000270329 
## ... Similar to previous best
## Run 12 stress 9.798048e-05 
## ... Procrustes: rmse 0.0001144515  max resid 0.0004243048 
## ... Similar to previous best
## Run 13 stress 9.98246e-05 
## ... Procrustes: rmse 8.444349e-05  max resid 0.0004618941 
## ... Similar to previous best
## Run 14 stress 9.955774e-05 
## ... Procrustes: rmse 0.0001026056  max resid 0.0004400828 
## ... Similar to previous best
## Run 15 stress 9.889913e-05 
## ... Procrustes: rmse 7.846163e-05  max resid 0.000279398 
## ... Similar to previous best
## Run 16 stress 9.731138e-05 
## ... Procrustes: rmse 8.529584e-05  max resid 0.0002259614 
## ... Similar to previous best
## Run 17 stress 9.410327e-05 
## ... Procrustes: rmse 6.725978e-05  max resid 0.0002614167 
## ... Similar to previous best
## Run 18 stress 9.432414e-05 
## ... Procrustes: rmse 7.68446e-05  max resid 0.000506901 
## ... Similar to previous best
## Run 19 stress 9.893589e-05 
## ... Procrustes: rmse 8.42744e-05  max resid 0.0002169461 
## ... Similar to previous best
## Run 20 stress 9.898755e-05 
## ... Procrustes: rmse 8.362943e-05  max resid 0.000181727 
## ... Similar to previous best
## *** Solution reached

5.4 tSNE

The ‘tSNE’ plot was not called within the shiny application. Use default settings.

Use the settings

  • x-axis = X1,
  • y-axis = X2,
  • Perplexity = 10,
  • Number of iterations = 1000,
  • Number of retained dimensions in intial PCA = 10,
  • Output dimensionality = 3, scale = TRUE,
  • center = TRUE, and
  • Highlight = none.

5.5 UMAP

The ‘UMAP’ plot was not called within the shiny application. Use default settings.

Use the settings

  • x-axis = X1,
  • y-axis = X2,
  • Minimum distance = 0.1,
  • Number of neighbors = 15,
  • Spread = 1, and
  • Highlight = none.